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AI Multimodal Protein–Compound Screening Service

AI-Powered Multimodal Protein–Small Molecule Docking & Virtual Screening

Screen up to 1,000,000+ compounds against your protein target in 20 days using machine learning and 3D structural docking. Identify high-affinity leads with ranked binding free energy analysis — dramatically accelerating drug discovery timelines.

Zero Experimental Cost
Confidence-Scored Results
Publication-Ready Figures
Wet-Lab Validation Available
24h Scientific Support

Service Overview

ICDMO's AI Multimodal Protein–Compound Screening Service employs machine learning and deep learning to analyze protein–small molecule interactions, leveraging three-dimensional protein structures to predict binding poses and affinities with superior speed and precision. The platform integrates Vina batch docking, ML-based scoring functions, and multimodal protein representation (3D structure + sequence + physicochemical properties) to deliver highly accurate virtual screening results. Applicable to drug mechanism investigation, enzyme substrate recognition, signal transduction analysis, and lead optimization.

Technical Advantages

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High-Throughput Virtual Screening
Screen up to 1 million compounds in 20 days using batch Vina docking with ML-enhanced scoring — identify top leads rapidly.
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Cost-Effective Drug Discovery
Replace expensive and time-consuming experimental screening with accurate computational predictions for initial hit identification.
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Multimodal AI Integration
Combines protein 3D structure, sequence features, and small molecule physicochemical properties for comprehensive interaction analysis.
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Accurate Binding Affinity Ranking
Results ranked by binding free energy from Vina docking — top 5 models visualized with 3D distant/close-up views and 2D interaction diagrams.
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Flexible Input Formats
Accepts protein 3D structures or amino acid sequences; small molecules in 2D or 3D formats (mol2, sdf, pdb, SMILES).
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Seamless Downstream Validation
Top hits from virtual screening validated experimentally via SPR, MST, BLI, ITC, and cell-based assays.

Key Applications

Protein–Small Molecule Compound Docking

▸Drug mechanism investigation: understand how lead compounds engage target binding pockets
▸Enzyme–substrate recognition: identify substrate specificity determinants and inhibitor binding modes
▸Signal transduction: map allosteric sites and modulator binding to signaling proteins
▸GPCR and ion channel compound screening

Protein–Protein Interaction (PPI) Modulation

▸Identify small molecules that disrupt or stabilize protein–protein interfaces
▸Screen compound libraries against PPI hot spots for inhibitor discovery
▸AI-based analysis of PPI networks to discover novel drug targets

Virtual Screening & Hit Identification

▸Screen FDA-approved compound libraries for drug repurposing opportunities
▸Screen proprietary compound collections against novel targets
▸Fragment-based screening for lead generation
▸Natural product library screening

Sample Submission Requirements

1Protein: 3D structure (PDB file) preferred; amino acid sequence accepted (structure will be modeled)
2Small molecules: 2D or 3D structural files (mol2, sdf, pdb, or SMILES string)
3Optional: Known binding pocket coordinates (box center + dimensions) for focused docking
4For large compound libraries (>10K): provide as SDF or SMILES database file

Docking Pipeline (Case Study: CYP51 + FDA Compounds)

1Step 1 — Obtain pdbqt files: Prepare receptor (PDB → pdbqt) and ligand (2D/3D → pdbqt) files using AutoDock Tools
2Step 2 — Define docking box: Confirm box size and center coordinates around active site (e.g., CYP51 heme binding cavity)
3Step 3 — Batch molecular docking: Run Vina batch script across all compounds; generate binding affinity data for each pose
4Step 4 — Ranking and selection: Sort all compounds by binding affinity (kcal/mol); select top 5 models for detailed analysis
5Step 5 — Generate visualizations: 3D distant view, close-up interaction view, and 2D interaction diagram for each top candidate

Service Timeline & Deliverables

Service ScopeTurnaroundDeliverables
≤150,000 compounds screened against target7 working daysAnalysis report PDF; ranked compound list with binding affinities; top 5 docking visualization images (3D + 2D interaction diagrams)
150,000–1,000,000 compounds screened20 working daysFull virtual screening dataset; top candidates with structure–activity insights; docking score distribution analysis
Custom: PPI inhibitor screeningQuoted on requestPPI hot spot analysis + compound screening results
Optional: MD validation of top hits+15 days per compoundMD trajectory, binding stability analysis, MM/GBSA confirmation

Service Process

1
Online Consultation
2
Solution Matching
3
Service Contract
4
AI Computation
5
Project Report

Note: All services are for research use only and not intended for diagnostic or therapeutic purposes.

Get a Custom Quote

Our scientific team responds within 24 hours with a detailed technical proposal and pricing tailored to your research goals.

Contact Us Online Consultation

Standard Deliverables

✓Detailed analysis report (PDF)
✓Raw data files & processed outputs
✓High-resolution publication figures
✓Interaction scoring tables (Excel)
✓Project summary presentation

Related AI Services

Molecular Dynamics SimulationProtein Interaction & Binding Site PredictionDigital Library-to-Library ScreeningDigital Protein/Nucleic Acid Interaction ModelTarget-based Drug DiscoveryDrug Screening & Profiling
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